chrX-140503764-C-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_005634.3(SOX3):c.1297G>T(p.Ala433Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000316 in 1,170,049 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 12 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 11/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (no stars).
Frequency
Consequence
NM_005634.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000267 AC: 3AN: 112355Hom.: 0 Cov.: 23 AF XY: 0.0000579 AC XY: 2AN XY: 34531
GnomAD4 exome AF: 0.0000321 AC: 34AN: 1057694Hom.: 0 Cov.: 31 AF XY: 0.0000295 AC XY: 10AN XY: 339522
GnomAD4 genome AF: 0.0000267 AC: 3AN: 112355Hom.: 0 Cov.: 23 AF XY: 0.0000579 AC XY: 2AN XY: 34531
ClinVar
Submissions by phenotype
Premature ovarian insufficiency Uncertain:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at